−n

match only the characters a, c, g, or t they can be in upper or in lower case

−l

set the minimum length of a match. The default length is 50

−b

compute forward and reverse complement matches

−r

only compute reverse complement matches

−c

report the query−position of a reverse complement match relative to the original query sequence

−F

force 4 column output format regardless of the number of reference sequence input

−L

show the length of the query sequences on the header line

−d

set the split size. The default value is 1

−t

number of threads. The default is 1 thread

−h

show possible options